Is there a way to it?
Dear Modellers, Is there a key to increase gap penalty scheme for different factors, like residue compatibility, Solvent Accessible Surface Area, depth of residue center from the molecular surface etc.
Your help is appreciated. Ashish
Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA
On 01/10/2012 02:05 AM, Ashish Runthala wrote: > Is there a key to increase gap penalty scheme for different factors, > like residue compatibility, Solvent Accessible Surface Area, depth of > residue center from the molecular surface etc.
Sure, if you're using SALIGN, you can simply adjust the weights (feature_weights argument). "Residue compatibility" is feature 1; surface area is roughly feature 3. For features that SALIGN doesn't consider (presumably that's what you mean by "etc" above) you would have to calculate them yourself and give SALIGN a user-defined weight matrix (feature 6) to use.
Ben Webb, Modeller Caretaker
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